Significance Monitoring and controlling the genetic structure of non-human primate breeding colonies and reconstructing/confirming genealogical relationships in the colonies are essential to the maintenance of non-human primates as a research resource. Objectives To develop rapid and inexpensive methods to conduct paternity exclusion analysis and estimate kinship and inbreeding coefficients and parameters of genetic subdivision and gene diversity in groups of non-human primates. Results Eighteen new highly polymorphic microsatellite (STR) loci were identified and genotypes of 40 unrelated rhesus males were characterized for each of these loci. Gene diversity (H) estimates of these loci range between 0.11 and 0.87. The value of H for the 12 most informative of these was 0.77 ((0.07) and ranged between 0.67 and 0.87; these loci exhibited, on average, 7.3 ((2.4) alleles per locus. These 12 STR loci, together with 15 STR loci previously reported were used to genotype 13 members of an extended family to attempt to differentiate known relative pairs by the number of STR alleles shared in common using these 27 loci. Unrelated pairs were easily differentiated from all related pairs. These results suggest that STR loci can be useful in reconstructing unknown pedigrees in groups with missing or incomplete records. These same loci were screened for a sample of 60 orangutans and nine highly polymorphic loci were used to compare orangutans of different geographic o rigins within Bornco and within Sumatra. Future Directions The STR loci cited above will be used to screen a variety of other cereopithecoid species including patas, vervet, and howler monkeys and orangutans to assess their effectiveness for genetic management, and mother/offspring pairs of rhesus in a group of rhesus monkeys will be screed for all 27 hypervariable STR loci to estimate the incidence of mistaken maternity in rhesus groups. KEY WORDS microsatellite (STR) loci, PCR amplification, paternity exclusion analysis (PEA) FUNDING NIH Grant RR00169 PULBLICATIONS Kanthaswamy, S., Smith, D. G. Use of microsatellite polymorphisms for paternity exclusion in rhesus macaques (Macaca mulatta). Primates 39(2):135-145, 1998.